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Sample GSM710266 Query DataSets for GSM710266
Status Public on Aug 02, 2012
Title dorsal pancreatic epithelia-e12.5-MUT-4
Sample type RNA
 
Source name dorsal pancreatic epithelia e12.5
Organism Mus musculus
Characteristics strain: Sox9-flox [mixed FVB/N x C57Bl/6J background] X Pdx1-Cre [C57Bl/6J background]
tissue: dorsal pancreatic epithelia
developmental stage: e12.5
genotype: Sox9 mutant
Growth protocol All animal experiments described herein were approved by the University of California, Irvine and San Diego Institutional Animal Care and Use Committees. For timed matings, noon on the day of vaginal plug appearance was designated e0.5.
Extracted molecule total RNA
Extraction protocol E12.5 dorsal pancreatic epithelia were manually microdissected and stored in 50 μl of RLT lysis buffer (QIAGEN, Valencia, CA) in the –80°C freezer. Each individual RNA sample was collected from three dorsal pancreata (i.e. three embryos) as per the manufacturer's instructions. We prepared RNA samples in ~12 μl of DEPC-treated water. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
Label Cy3
Label protocol Approximately 250 ng of total RNA was amplified and labeled with Cy3 using the Low RNA Input Linear Amp Kit PLUS, One-Color (Agilent Technologies, Santa Clara, CA). This labeling reaction produces 0.25 – 2.0 μg of Cy3-labeled cRNA (anti-sense), by first converting mRNA primed with an oligo (d)T-T7 primer into dsDNA with MMLV-RT and then amplifying the sample using T7 RNA Polymerase in the presence of Cy3-CTP.
 
Hybridization protocol 1.65 μg of cRNA was fragmented and hybridized to the array for 17 hr. at 65°C then washed.
Scan protocol Arrays were scanned with the AgilentTechnologies Scanner G2505B US23502332 using protocol version GE1-v5_95_Feb07
Description 251486817349_3.txt
Data processing Mean foreground intensities were obtained for each spot and imported into the mathematical software package “R”, which is used for all data input, diagnostic plots, normalization and quality checking steps of the analysis process using scripts developed in-house by Peter White specifically for this analysis. In outline, the Cy3 (green) intensities were not background corrected (this has been shown to only introduce noise), and corrected for the scanner offset (40 was subtracted for each intensity). The dataset was filtered to remove positive control elements and any elements that had been flagged as bad. Using the negative controls on the arrays, the background threshold was determined and all values less than this value were set to the threshold value. Finally, the data was normalized using the Limma Quantile Normalization package in “R” (Smyth 2004, Bolstad et al., 2003).
 
Submission date Apr 16, 2011
Last update date Aug 02, 2012
Contact name Brandon Taylor
Organization name University of California, San Diego
Department Pediatrics and Cellular & Molecular Medicine
Lab Maike Sander, M.D.
Street address Sanford Consortium for Regenerative Medicine, 2880 Torrey Pines Scenic Dr., Room 3101
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platform ID GPL4134
Series (2)
GSE28669 Identification of Sox9-Regulated Pathways During Early Pancreas Organogenesis
GSE28671 Identification of Sox9-Regulated Pathways During Pancreas Development

Data table header descriptions
ID_REF
VALUE Log2 normalized signal intensity

Data table
ID_REF VALUE
12 63
13 114
14 68
15 71
16 468
17 62
18 65
19 108
20 69
21 661
22 71
23 282
24 121
25 372
26 84
27 869
28 148
30 72
31 83
32 61

Total number of rows: 33067

Table truncated, full table size 315 Kbytes.




Supplementary file Size Download File type/resource
GSM710266.txt.gz 9.2 Mb (ftp)(http) TXT
Processed data included within Sample table

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